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Method and test kit for quantitative determination of polynucleotides in a mixture
8143388 Method and test kit for quantitative determination of polynucleotides in a mixture
Patent Drawings:Drawing: 8143388-10    Drawing: 8143388-11    Drawing: 8143388-12    Drawing: 8143388-13    Drawing: 8143388-14    Drawing: 8143388-15    Drawing: 8143388-16    Drawing: 8143388-17    Drawing: 8143388-18    Drawing: 8143388-19    
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Inventor: Soderlund, et al.
Date Issued: March 27, 2012
Application: 12/105,960
Filed: April 18, 2008
Inventors: Soderlund; Hans (Espoo, FI)
Satokari; Reetta (Helsinki, FI)
Kataja; Kari (Espoo, FI)
Takkinen; Kristiina (Espoo, FI)
Assignee: Valtion Teknillinen Tutkimuskeskus (Espoo, FI)
Primary Examiner: Martinell; James
Assistant Examiner:
Attorney Or Agent: Arent Fox LLP
U.S. Class: 536/24.3; 435/6.1; 435/6.11
Field Of Search:
International Class: C07H 21/04; C12Q 1/68; C12N 15/11
U.S Patent Documents:
Foreign Patent Documents: 99/37663; 02/055734
Other References: Jerry Olejnik, et al.; "Photocleavable peptide-DNA conjugates: synthesis and applications to DNA analysis using MALDI-MS"; Oct. 8, 1999;Nucleic Acids Research; vol. 27, No. 23, pp. 4626-4631. cited by other.
Narayana R. Isola, et al.; "MALDI-TOF Mass Spectrometric Method for Detection of Hybridized DNA Oligomers"; May 1, 2001; Analytical Chemistry, vol. 73, No. 9 , pp. 2126-2131. cited by other.
Amann et al.;1990 Applied and Environ Microbiol, 56: 1919-1925. cited by other.
Chen-Liu et al., 1995, Genomics 30: 388-392. cited by other.
P. Eric Mayrand et al.: "Automation of Specific Human Gene Detection," Clin. Chem., vol. 36, No. 12, 1990, pp. 2063-2071. cited by other.
Tenhunen et al.: "A solution hybridization method for quantification of mRNA determining the amount and stability of oncogene mRNA;" Genetic Analysis Techniques and Applications (8): 228-33 (1990). cited by other.
Zhang et al., "Reconstruction of DNA sequencing by hybridization,"Bioinformatics, vol. 19, No. 1, 2003, pp. 14-21. cited by other.
Isola et al., "MALDI-TOF Mass Spectrometric Method for Detection of Hybridized DNA Oligomers," Analytical Chemistry, 73(9):2126-2131 (2001). cited by other.









Abstract: The invention relates to a method and test kit for quantitative determination of the amounts or relative proportions of polynucleotides in a mixture. The invention enables assessment of dynamic variations in a mixed population of organisms using affinity aided solution hybridization. The test kit comprises organized pools of polynucleotide probes having approximately the same number of nucleotides, which are distinguishable using resolution enabling tags providing the probes with different sizes. The resolution enabling tags may simultaneously act as tracer, affinity or primer tags. The probes are allowed to hybridize with affinity tagged analyte polynucleotides. The result is hybrids, recoverable on separation aiding tools provided with counterparts of the affinity tag. After the quantitative release of the probes, the individual probes can be amplified and recorded. The method and test kit are useful for determining hygienic and epidemiologic situations and evaluating the effect of antibiotic treatment and sanitary measures.
Claim: The invention claimed is:

1. A test kit for use in a method for determining amounts or relative proportions of more than one individual polynucleotide sequence in a sample comprising a mixtureof target polynucleotide sequences using a quantitative affinity aided solution hybridization with more than one polynucleotide probe, the test kit comprising: one or more probe pools, each pool comprising more than one soluble tracer-taggedpolynucleotide probe, wherein each single tracer-tagged polynucleotide probe is complementary to an individual target polynucleotide sequence in the sample, each tracer-tagged polynucleotide probe has approximately the same number of hybridizingnucleotides as the individual target polynucleotide sequence in the sample, and each tracer-tagged polynucleotide probe is provided with one or more resolution enabling tags, which provide the tracer-tagged polynucleotide probes with different mobilitiesin fractionation, separation or recording systems; one or more vessels, wherein each pool of polynucleotide probes is placed in its own vessel, wherein when multiple vessels are provided, they may be separate or joined together; and apparatus forseparating said tracer-tagged polynucleotide probes, wherein the amount of more than one individual polynucleotide sequence in a sample is determined by releasing tracer-tagged polynucleotide probes from hybrids comprising the individual polynucleotidesequence and the tracer-tagged polynucleotide probes captured by said apparatus, conducting size fractionation of the tracer-tagged polynucleotide probes, recording the resolution enabling tags provided on said tracer-tagged polynucleotide probes, andcalculating the amount of said released, tracer-tagged polynucleotides using size and concentration standards, wherein the amount of the released polynucleotide probes corresponds to the amount of the complementary target polynucleotide sequences whichhave hybridized thereto.

2. The test kit according to claim 1, wherein for the determination of dynamic variations in the amounts or relative proportions of polynucleotide transcripts or their subgroups in an individual organism, the soluble tracer-taggedpolynucleotide probes comprise sequences that hybridize with polynucleotide sequences selected from the group consisting of a conserved or hypervariable region from intragenomic sequences specific for subgroups, species, or subspecies of transcriptsexpressed in the organism, and further comprise one or more resolution-enabling tags that are separable in a sieving medium.

3. The test kit according to claim 1, wherein the resolution enabling tag is selected from the group consisting of a tracer tag, an affinity tag, and a primer tag, and combinations thereof.

4. The test kit according to claim 3, wherein the number of soluble tracer-tagged polynucleotide probes in the pool is more than five.

5. The test kit according to claim 3, wherein the soluble pools of tracer-tagged polynucleotide probes are placed in wells on a microtiter plate.

6. The test kit according to claim 1, wherein the polynucleotide probes are selected from the group consisting of DNA fragments, synthetic peptidic nucleic acids (PNAs), and locked nucleic acids (LNAs).

7. The test kit according to claim 1, wherein for a comparative, quantitative assessment of variations in the amounts or relative proportions of individual target polynucleotide sequences in a mixture of polynucleotide sequences, the test kitcomprises a set of multiple test kits, wherein at least one identical test kit having identical pools of polynucleotide probes is provided for each sample to be compared.

8. The test kit according to claim 7, wherein each individual test kit in the set of multiple test kits is provided with tracer tags, which are distinguishable from each other by the emitted signal.

9. The test kit of claim 1, wherein the kit further comprises an affinity-tagged probe.

10. The test kit of claim 9, wherein the affinity tag of the affinity-tagged probe comprises oligo-dT.

11. The test kit of claim 9, wherein the affinity tag of the affinity-tagged probe comprises a sequence-specific probe.

12. The test kit of claim 1, wherein the apparatus for separating the tracer-tagged polynucleotide probes is a separation aiding tool provided with a counterpart of the resolution enabling tag.

13. A test kit for use in a method for quantitatively determining the amounts of multiple analyte polynucleotides present in a cell or tissue sample by applying affinity aided solution hybridization, comprising: one or more probe pools, eachhaving more than one different soluble tracer-tagged polynucleotide probe provided therein, wherein each soluble tracer-tagged polynucleotide probe is provided with a distinct size allowing its identification and recording, and each single solubletracer-tagged polynucleotide probe is complementary to an analyte polynucleotide sequence to be quantitatively determined, optionally two terminal primer tags for each of the tracer-tagged polynucleotide probes, a vessel for each probe pool having morethan one soluble tracer-tagged probe polynucleotide provided therein, wherein each pool is placed in its own vessel, which vessels are separate or joined together, at least one affinity tag to attach to an analyte polynucleotide sequence to bequantitatively determined, and a separation aiding tool provided with the affinity pair of the affinity tag.

14. The test kit according to claim 13, wherein the soluble tracer-tagged probe polynucleotides are provided with at least two terminal primer tags that allow them to be amplified by PCR after separation from the analyte polynucleotidesequence.

15. The test kit according to claim 14, wherein the test kit is optionally provided with a separate set of optionally tracer tagged primers or a separate set of tracer tags.

16. The test kit according to claim 13, wherein the separation aiding tool is selected from a group of solid supports consisting of microparticles, microbeads, latex particles, magnetic particles, threads, pegs, sticks, microwells and affinitycolumns.

17. The test kit according to claim 13, wherein the probe polynucleotides are selected from the group consisting of DNA fragments, synthetic peptidic nucleic acids (PNAs), and locked nucleic acids (LNAs).

18. The test kit according to claim 13, wherein each vessel is a well of a microtiter plate.

19. The test kit according to claim 13, wherein for a comparative, quantitative assessment of variations in the amounts or relative proportions of individual target polynucleotide sequences in a mixture of polynucleotide sequences, the test kitcomprises a set of multiple test kits, wherein at least one identical test kit having identical pools of tracer-tagged polynucleotide probes is provided for each sample to be compared.
Description:
 
 
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